Metroid: Origins
by Chaos242
Summary: Samus is thrown into a newly revived war between the Pirates and Federation.  When the Pirates start making bolder moves even after their army has been cut in half, Samus and the crew of the Ragnarok investigate.  Post Corruption, pre Metroid II. R&R plz
1. Chapter 1

Metroid Origins

Derek Hylio was sleeping pleasantly onboard the GFS Olympus, well not exactly sleeping, just quietly thinking.

_"How often is it that I actually get some sleep now-a-days? I wonder when the Ragnarok will have its maiden voyage. When am I am going to get that arm-cannon upgrade that Jake promised..._

Derek's thoughts were abruptly stopped as an alarm blared throughout the_ Olympus, _all of the crew was suddenly awake and on their feet.

Admiral Dane's voice came onto the comm. system "Wake up Marines, We just got an urgent distress signal From Samus Aran on a planet outside of Federation space, She has located a pirate compound that is too much for her to handle...I am ordering the _Ragnarok _to warp to Aran's coordinates, Prep the ship and get going."

"_Maiden voyage indeed! Why do I always get what I wish for at the wrong time?"_

Samus ran at full speed across the barren wasteland that the pirates had made out of the planet that once was a refuge for the Chozo that fled Zebes, the land was a hard, black volcanic glass, it was rough in some parts and smooth in others. Lining the black ground were strangely shaped mountains of what was once metal from Chozo households and buildings of other sorts, _whatever they were_, Samus had thought,_ They are unrecognizable now. _But Samus wasn't thinking about those former buildings now, now she was running, not because of the pirates that were only meters behind her, but because of what the pirates were running from, A Parasite queen, not only that but a parasite queen that is of the "plated" variety, in short, neither Samus nor the thirty-some pirates behind her had the concussive weapons able to kill it.

_"Figures that I would attack some random experiment before learning that I couldn't kill it, and figures that the pirates weren't smart enough to build a way of controlling it, and were the hell is Dane, never on time, ugh, If I get out of this I am personally going to explain to him how to build a Chozodian warp engine."_

The plated parasite queen stopped suddenly, Both Samus and the pirates did the same. The Queen looked up into the sky for a few moments and then, with a grunt charged twice as fast as it had before at the pirates and Samus. Some of the Tallonian pirates open fired but their shots bounced harmlessly of the Queen's plated carapace, Samus rolled into morph ball and then unfurled as the Queen charged past her. The Queen, with one of the Tallonian pirates impaled on one of its galvanized legs, slowly disappeared from view. Samus Then turned to the remaining 30-some pirates that consisted of Tallonian and a few Utrazonian militias. She took aim at the nearest militia and was about to fire when an ear-piercing screech made her shudder and wince; the pirates were on the ground screaming in agony as they didn't have sound filtering helmets. The screech was followed by an explosion that knocked Samus backwards, when she got up there was a gaping crater in the ground where the majority of the pirates had been, she also noted that the pirates' numbers were now reduced to four, one of them got up, only to be impaled by a falling shard of volcanic glass. Samus looked for the source of the explosion and first saw a ship about one third the size of the _Olympus,_ It was roughly shaped like her old hunter class that she had used on Tallon IV. Samus then saw a dot that grew to a black blur before crushing the three remaining pirates. _A tank?_ Samus thought, it was black with a two meter long cannon protruding it and a turret on top of it. Several federation troopers exited the tank; one went on top of it and manned the turret that slightly resembled a hydra class. One of the troopers was wearing armor that mirrored the Power suit in every way, except that it had a blue visor, with federation colors and insignias.

"Samus it's good to see that you're unscathed," Said the trooper in the power suit copy.

_"Unscathed, I almost got crushed by a parasite Queen and shot by your missile"_ _Thought Samus grimly_

_"_We got word that you had some trouble and came to help, sorry about the missile, we had to cut it close, or those pirates would have been hard to beat. What is your situation?"

"My ship detected a massive burst of nuclear energy, After searching the planet I discovered a pirate research facility, I tried to infiltrate it but was forced to retreat after a less than cordial encounter with a Plated Parasite queen and about thirty pirate troopers." explained Samus

"Where is this Parasite queen now?"

"It was heading towards the source of the nuclear energy burst," Said Samus, while motioning in the direction that it went. "Plated queens are only vulnerable to concussive weapons, so I'm out of options."

The trooper put his hand on his chin and looked downward in thought, but his thoughts were short lived as an Areotrooper Flew over the large mound of twisted metal and fired at the marines. The marine on the turret shot at the Areotrooper, sending it into evasive actions. As the marine's and Samus's attention were on the Areotrooper an Pirate militia that was under the tank decided to make his escape, it's legs were broken so it pulled itself along the shattered volcanic glass for a few feet and reached for a plasma rifle dropped by a now dead Utrazonian. Then another dot appeared in the sky before crushing the pirate militia's weapon and forearm. Samus turned to look at this new federation weapon and found that it wasn't federation at all but rather Luminoth, an Ingsmasher with another power suit wearing trooper sitting in a seat on the back of the Ingsmasher, fingering a large cannon that was similar to the ice beam. The new Ingsmasher lumbered away to one of the two pathways through the metal mountains.

"Concussive eh," said the first power suit marine. "I know somebody who can do that, but first I have to secure the area."

As he finished speaking a normal marine stepped up to him and saluted.

"What are your orders Captain Skylar?" Asked the marine in a high pitched female voice.

"Fauna, good, you take the drones and go to the pathway opposite Jake and disguise yourself as a pirate, Go!"

Samus was about to ask how Fauna was going to disguise herself when she changed shape to a Utrazonian pirate and ran to the pathway with five or six "Jolly-roger" shaped drones following her.

"Samus I am going to stay here with the troops and hold the area, I'm sending you in with Derek, my demolitions expert, he has the weaponry to fight your parasite queen, He will meet you at the compound up ahead in one minute, you had better get going"

Without a word Samus bolted strait for the compound that loomed up ahead, her mind burred with questions.

_"Was that '"Fauna'" marine one of Gandrayda's kind? How do those troopers have my weapons and armor, and how did that Jake trooper get an Ingsmasher?"_

Regardless, Samus didn't have the time to get these questions answered now, so she kept on running towards the ever nearer compound.

As Samus left the area where the marines had landed, the still living pirate militia managed to get onto his knees only to be hit by the suicide diving Areotrooper that the marine at the tanks turret finally killed.

The sound of pirate screams and weapon fired clouded her hearing, but Samus didn't let it affect her, she now had a clear objective and was doing what she had always done, kill pirates, save the galaxy etc. The only thing out of place in Samus's mind was how the federation was able to duplicate her power suit; the humans were still just breaking the surface of what the Chozo had established years ago, so they couldn't have made a power suit.

_"I never gave them any information on Chozo tech, they aren't ready for that power yet, they needed to find their own way, that's how it should have been. The only way the federation could have gotten our tech would be from a...could they have found a living Chozo, no, not even I can find them, maybe they found some Chozo tech and replicated it, yeah that's it, they just found some Chozo artifact...before me...right."_

Samus had finished her thoughts just as the pirate compound came into view. A sudden beep made Samus jump until she realized that it was a radio call, she pressed a button on her helmet.

"Samus, come in. This is Captain Skylar, we are holding the area but the pirates are mobilizing, we are outnumbered, so whatever you're going to do, do it soon. Using the information sent to us by your ship, the _Ragnarok _has located the source of the nuclear radiation. Its origin is a pirate _Colossus _class battleship that seems to have crash landed on this planet; our readings indicate that the radiation is an exact match to your files on the "Omega cannon". It is protected by a large energy shield so we cannot destroy it using the _Ragnarok's_ weapons easily, we need you and Derek to infiltrate the pirate facility and deactivate that shield, and if you can find a way to destroy the _Colossus _in the process it would be much appreciated. Skylar out."

Samus nodded to herself and continued toward the compound. As the compound came into view Samus noted the gaping hole in the main entrance.

"I guess that means the Queen was here." She muttered to herself

As she approached a firefight came into view, five Tallonian pirates were shooting at two demolition troopers and one marine in a power suit that bore brown-black colors and a yellow visor. Samus assumed that the power suited one was the Derek that Skylar had told her about. She ran to aid the marines and watched the fight as she approached; they were still out of her range. Derek shot power beams in five shot bursts at the pirates, killing two, the pirates responded by riddling one of the demolition troopers with charged energy bolts. The remaining demolition trooper knocked a pirate down and shot it in the skull repeatedly until it was just green and red mush. One of the remaining pirates leapt at Derek with its scythe over-head, Derek drew an energy charged blade from a scabbard on his back, the pirate's scythe held for a few seconds before Derek's blade sliced the scythe in two, Derek then proceeded to cut the pirate in half. Samus made it up to a meter away from Derek and the remaining demolition trooper.

"Samus, it's about time you showed up," Said Derek in a gruff voice. "We were about to be overwhe..."

His sentence was cut short as Samus shot the last pirate that was about to behead Derek.

"You're welcome." replied Samus.

"Ok, a huge...thing came through here earlier, know anything about that?" asked Derek

"Yeah, it was a plated parasite queen, it can only be injured with concussive weapons, Skylar said that you were the man to come to about that."

"Oh, well concussive is my specialty."

"Let's move then." With that Samus and Derek were off leaving the Demolition trooper behind to guard the compound.

The compound was dark and the sounds of battle outside were snuffed out by the sound of the queen's dying victims, them being several dozen pirates of all breeds and one very unlucky Shegoth. The queen's roars were endless, and grew ever louder as Samus and Derek closed in on it.

"So, you had experience with these queens before?" asked Derek.

"Yes, once on the pirate frigate _Orpheon_ I killed a normal parasite queen, it was...difficult" answered Samus.

They ran into a room filled with broken storage tubes that were modified for experiments. Then the queen appeared, it was clinging to the ceiling. It roared as acid dripped from its double mandibles.

"So you don't like concussive, try this!" yelled Derek as his arm cannon changed to the same shape as Samus's missile launcher.

"Ha" cried Derek as morph ball bombs shot from the cannon in bursts of three.

Samus shot her power beam at the queen, just to distract it, she watched as the bombs took their toll on the queen, each hit took a few more units of health away from the queen, it was not going to be enough.

The queen shot a stream of weapon grade acid at Derek who writhed in pain, Samus rolled into morph ball and laid as many bombs as she could before uncurling and resuming her power beam shots, one lucky shot caught the queen in the mouth, stopping the beam of acid that was on Derek.

Derek stood up and charged up with the power beam.

"Now you pissed me off!", With that the arm cannon changed again to bomb mode but instead of a bomb the charged shot merged with the morph ball bombs and shot a power bomb at the queen, damaging it heavily. Samus took the opportunity to roll into morph ball and go inside the parasite queen via getting swallowed.

"Samus!" yelled Derek before the parasite queen exploded from the inside out and Samus walk casually towards Derek who was covered in green slime.

"Oh I bet you think that covering your allies in slime is real funny Samus, but I don't, so please, don't do it again."

"Just trying to help." said Samus.

They then abandoned the compound and walked into a windowed room with a large terminal in it.

"This must be the control center." Exclaimed Samus.

"Uh Samus?" said Derek from the window. "You might want to have a look at this."

As Samus walked over she saw a massive _Colossus _class ship supported by machine arms that lifted it and aimed it to a dot in the sky.

"It's aimed towards the _Ragnarok,_ we have to stop it!" yelled Derek

Samus went back to the terminal and started scanning it.

"It's in a pirate dialect that I can't translate." said Samus

Just then a pirate militia jumped at Samus who then shot it once in the skull.

Derek, ignoring the surprise attack that Samus just thwarted, ran to the terminal and started shooting it with morph ball bombs, causing it to spark.

"What are you doing!" exclaimed Samus

Then the terminal spoke in plain English, "_Colossus self-destruct selected, DNA verification required to activate self-destruct."_

"Shit, where are we going to get pirate DNA?" yelled Samus.

Derek picked up the dead militia and dragged it towards the terminal, when he placed it in the terminal. Nothing happened, so he began to slam it into the terminal, still no effect.

"Damn it! What DNA does it want, Wait, it spoke English, aha." Exclaimed Derek. He then put his hand on the terminal.

_"Colossus self destruct activated"_

"How did that work?" asked Samus.

"Those stupid pirates stole this terminal from humans."

"I guess that's why they call them pirates."

Samus and Derek turned to the window and watched as the pirates ran with flailing arms away from the ship as it created a small nuclear explosion. Derek winced and clutched his side as the explosion reached its peak and died.

"Are you alright?" asked Samus

"Fine, my suit just isn't as well shielded as yours"

Samus reached for her helmet as a radio call came in.

"Samus, job well done, you couldn't have cut it any closer, are you and Derek alright?" asked Skylar

"Fine Captain, do I have permission to recoup onboard the _Ragnarok_?" asked Samus, knowing that they could not say no

"It would be an honor." replied Skylar.

But Samus wasn't interested in recouping, she had questions that needed answering, specifically about their power suit, and she would get them, one way or another.


	2. Chapter 2

Chapter 2

Samus and Derek walked out of the Pirate compound, past the corpse of the Parasite Queen, and outside. They met up with the demolition trooper, who was still guarding the entrance, and continued back to the area where Captain Skylar had fought the main pirate force. Several Federation troopers where dead, others were on medical stretchers and were being lifted to the _Ragnarok_ for advanced medical aid. The pirates were nowhere to be seen.

Skylar approached Samus and Derek, "Most of the pirates have retreated to their underground base, normally we wouldn't be able to reach them, but with the state-of-the-art weapons onboard _Ragnarok _we should be able to penetrate their defenses and kill most of them before they become a threat again. I've already given a full report to Admiral Dane, who is sending a cleanup crew to exterminate any remaining pirate threats on the planet once we leave orbit."

While Samus had stopped to listen to the report, while Derek continued walking towards the medical transports. He started checking the dead, turning off their helmets and looking at their faces.

"What is he doing?" asked Samus, "doesn't he want to hear the details of the battle?"

Skylar shook his head, "Derek doesn't care much for those kinds of things, he really just wants to finish the battle as quickly as possible and with as few losses as possible, he doesn't want to lose any of us."

"But isn't that what everyone wants?" asked Samus

"Well yes, but Derek is the kind of guy who would rather retreat than see his friends get hurt, even if it'll cost the Federation as a whole."

"Hmmm."

Skylar started towards the medical transports, he walked up behind Derek, who had been kneeling in front of one corpse in particular for a few minutes. He put his hand on Derek's shoulder and Derek got up and walked back towards Samus with Skylar. He sighed as he approached Samus.

"We lost Tim," said Derek, "it was his first week here, he was such a good kid."

"There are always great costs in war Derek, you of all people should know that, don't dwell on It." advised Skylar

Derek shook his head again and then looked into the sky. An Aries class troop transport landed near them. The ship was about 100 feet from exhaust to head. The front of the ship was a round head with a blue view port, meant to accustom one pilot. Parallel on both sides of the head were two huge cannons that were a good yard out from the main portion of the ship. Samus had seen what these transports were capable of during the invasion of the pirate home world during the last phazon crisis…

_Phazon crisis_

Samus looked out from window into the field filled with huge pirate turrets that guarded critical landing stations that were part of a huge checkpoint system that eventually lead to the planet core; which in turn led to the Seed, the Seed that had corrupted the planet and the pirates and turned them into pawns for Dark Samus to use to conquer and mutate the universe.

Samus shot the last power supply to the planetary shield that was keeping Admiral Dane and the seventh federation fleet outside of the planet's atmosphere. As she did, a pirate commando de-cloaked behind her and leapt at her with an energy blade. Samus turned just in time to dodge and counter the attack with a shot into the pirate's face. The pirate reeled backwards and then shot at Samus with phazon charged bolts from his main weapon. Samus took the hits and absorbed the phazon into her suit before going into Hyper-mode. Phazon coursed through her suit and burned her skin again, as it had been ever since she had absorbed the Phazon Seed on Elysia. She fired supercharged bolts of pure phazon energy into the pirate, disintegrating him completely.

Samus attempted to get out of hyper-mode but found that her 'exit hyper-mode' program had stopped working. The burning got worse, searing phazon began leaking into her skin and changing all the liquids under her skin into more phazon. The phazon began burning into her muscles. Her screams were muffled by the noise filter on her helmet, but to her the sound echoed again and again as she fought through the pain and shot phazon into the wall next to her. Outside, twenty Aries class transports landed, their main cannons firing into the pirate turrets and destroying them completely. Samus watched them as she shot phazon into the wall, draining the phazon from her arms and her suit until hyper-mode was forced to turn off. She kept thinking about how those blue concussive blasts from the ships looked like phazon, oh how she hated those blasts.

_Present_

Samus dismissed the memory of her role in the Phazon crisis and started towards the ship.

"_I'll wait until we're on the ship to ask them about the suits." _Though Samus, "_Then it won't be so easy for them to dismiss me."_

The transport took off, leaving the burnt and bloodied planet behind. Samus looked out the viewport and saw at least 5 other Aries-classes also leaving the planet.

"Are you pulling all of your troopers off the planet?" asked Samus.

"Yes, they don't need to be there anymore." Explained Skylar

Samus was confused, "Why? There's no way that Dane is already here!"

Skylar nodded, "No, he is not here yet, but we don't need to worry about the pirates on the planet anymore, you see in their haste to retreat they left their ships unattended. So we destroyed them."

As Skylar said this, Samus looked back to the planet and noticed a good number of pirates running on the ground looking for their ships.

"So you're just going to let them run free until Dane shows up?" asked Samus, "I still don't see the logic in this plan."

"You'll see once we get out of the first level of atmosphere." Said Derek

The ship pulled up and out of the first level of atmosphere. The pilot turned around and notified Skylar, who nodded.

"Do it" said Skylar

Suddenly a huge blue sphere of energy passed a few hundred yards from the ship and crashed into the planet's surface. The effect was immediate, the planet's crust was completely destroyed, magma poured from multiple cracks in the surface. Skylar cursed.

"I told them to leave the pirate compound outside of the blast radius!" complained Skylar, "Dane wanted to see firsthand what they were doing here."

Samus was frozen in place, "_W-what the hell was that weapon? How did the Federation come up with such power?"_

"Like it?" asked Derek, "I designed it myself."

Samus was still stunned, "I-I don't know what to say."

"Yeah, most people have that reaction first time they see it used." explained Derek, "I designed it using the same technology as the Omega cannon. Although your report on it didn't have much on the specifics, so I had to improvise."

"I've never seen a weapon like this used for an air to ground attack." Explained Samus

The ship was starting to exit the last layer of atmosphere.

"You should see what it's capable of when it's fully charged!" Said Derek, "This was just a basic shot."

Before Samus was able to continue her conversation about Derek's weapon, the _Ragnarok _came into view. It was about one third the size of _Olympus_ and looked distinctly like Samus's old Hunter-class mk1. Formed in an oval shape with a long viewport in the front of the ship, flat on the bottom for hover-landings and arched on the top to deflect attacks away from main systems. The differences were mostly in color, instead of the gold and green of Samus's old ship, this one was Federation gray and had blue tinted viewports. Their ship pulled into a docking bay which had opened for the ships in front of them. The bay was an exact match to the _Olympus _and had several troopers directing the landing and one posted in front of the main doors. A sudden call came over the intercom.

"Captain Skylar, Admiral Dane is waiting on communications deck 3, he's expecting a full report on how the mission went."

Skylar turned to Samus, "Would you please excuse me, I'd like to stay and talk but Dane is really strict when it comes to reports."

With that Skylar walked towards the main doors and was out of sight. Derek then motioned for Samus to follow him.

"I'll introduce you to our team." Explained Derek, "We were all handpicked by Dane; all of us are the best-of-the-best when it comes to our specific talents."

Derek deactivated his helmet which detracted into his torso armor. He pulled out a small device and pushed it into the door, which had a basic blue energy shield on it as most federation doors do on battleships. The shield deactivated and the round door split into three parts that retracted into the wall and then went back into position after they crossed through the invisible sensors to the other side. The blue shield also reappeared on the other side, this was the common way of function for all the doors, although they usually have varying shield powers, which are classified in strength using color, blue being the weakest and most basic form. They walked through that room and passed several mechanics doing maintenance checkups on the control panels. The viewports above the control panels showed ship after ship of one man Stiletto-Classfighters. The small, one man ships had two long stabilizers that hung in front of the forward viewport. The ships were being pulled along on conveyer belts, the viewport with the mechanics serving as a checkup station to see if there were any imperfections on the chassis of the ships.

They continued up the ramp into the next room, this one wasn't an exact replica of the Olympus, it was an elevator. Derek used the hand scanner and the elevator hologram activated in the middle of the platform, Samus stepped into it and the platform started moving down.

"Where are we going?" asked Samus

"To see my friend, Jake, I think you'll like him." Explained Derek, "He's the ship engineer, helped make the ship in the first place, and directs maintenance."

"Was he the guy on the Ingsmasher?" asked Samus

"Yeah, I figured you'd remember him from that thing."

The elevator stopped and Derek walked up to the door, which was orange. He pulled out the energy transmitter from before and pressed a switch on the side to increase the power it would expel. The door opened and they walked in, Samus was at once overtaken by the contents of the room. There were the 5 Aries class transports from earlier along with one Anhur class transport, which was essentially a small version of the Aries.

"Surprised?" asked Derek, "You should look above us."

Samus looked up and saw 3 Griffin class frigates. These ships were equipped with multiple Hydra class anti-aircraft turrets and one forward energy cannon that took up most of the ship's front half.

"Wow, I can't believe that you have so many smaller ships docked in this one." Said Samus

"Yeah, the _Ragnarok _is a real renaissance ship, it has the best tech for air to ground combat and space combat, along with its own mini-armada of vessels onboard." Explained Derek, "We were going to get another Aries class, but Jake simply wouldn't let us get rid of that old Anhur relic. He threatened to quit if we replaced it!"

Derek led Samus through the docking bay and up to another door, this one was green.

"Only the high ranking staff members, like me, are allowed access into this room." Explained Derek, "You'll be the first outsider to see what we have in here."

Derek put his arm-cannon into a slot next to the door in order to open it, this revealed a key pad into which Derek typed a code and gave his retinal scan.

"You guys really take security on this ship seriously." Stated Samus

"Yeah, this ship harbors all of the Federation's best kept secret projects and weapons, so security has to be tight."

The door opened and revealed wall of metal, Derek cursed under his breath.

"Jake, open the blast doors!" Yelled Derek, "I told you that those aren't necessary when we're off-duty!"

A muffled voice came from behind the doors, "What the hellja mean 'off-duty'? We just got outta major battle!"

"Just open the door!" said Derek, "I brought someone I think you'll like meeting."

Then came the sound of metal being pushed off of a desk and falling, followed closely by rapid footsteps. Suddenly a hole appeared in the door and a yellow eye could be seen through it. The eye moved from Samus to Derek, and then quickly back to Samus. There was a gasp and the door opened.

A hunched over man with one yellow eye stood there, despite his hunch he looked very young. His hair went in all different directions and there was a broad, toothy smile on his face. His hands clung to one another, as if they would die if they weren't in such a position.

"Samus Aran!" Exclaimed Jake, "I cannot believe it's really you!"

"Hi?" said Samus, "I didn't know I had a fan club."

"I'm not really a fan of you, more-so of your people." Explained Jake

"I presume that you're referring to the Chozo." Said Samus

Jake kept walking backwards and tripping over metal scraps that were piled all over the dimly lit room. He reached backwards and flicked a switch, turning on the lights. The room was at once much larger than Samus had originally thought it to be, covered in pieces of tech, some of which she recognized. Bryyoian tech, Elysian tech, Luminoth tech, even Chozodian tech. Jake turned around and hit a button which opened a hidden door.

"All of this stuff is just to distract any potential intruders, my real masterpieces are through here." Explained Jake

He led Samus and Derek through the door and into a huge room. The room's floor consisted of two huge blast doors. Next to them was the tank that Samus had seen earlier. Jake noticed Samus eyeing it.

"Recognize it?" asked Jake, "It'll be standard issue for the corps soon."

Samus noticed several boxed off areas that were sealed. "What's behind those?"

"My true works of art." Said Jake, he pushed button on a remote integrated into his wrist. The closest sealed box opened, revealing the Ingsmasher.

"Did you install the upgrades yet?" asked Derek

"Why yes, the main cannon is now multifunctional, capable of firing Ice beam shots, missiles, and a harpoon chord."

Samus looked at the Ingsmasher and the back to Jake, "Where and how did you get this?"

"It was my first project while I was stationed on Aether with the Luminoth." Explained Jake, "I volunteered to stay behind to help rebuild after everyone else was dismissed."

Samus was intrigued; she hadn't seen or heard from any of the Luminoth since she left Aether.

Jake continued, "U-Mos really took a liking to me, after I re-build this Ingsmasher. After that, well…"

He pressed all of the other buttons on the remote, revealing another Ingsmasher, several Quads, and finally a Quadraxis. The Quads were about twice the height of a person; with four wickedly sharp legs and a head the size of a watermelon, one eye looked blankly forward as the machine was offline. The Quadraxis was three times that size, with huge legs and a massive head.

"I've altered them all to support remote control and giving me the ability to drive them manually; they do still posses their old semi-sentient programming." Explained Jake

Samus looked all around her, surrounded by the enemies of her past, and suddenly smiled. _They're doing well, those big moths._ She thought while the memories came back.

_Aether mission_

The report of a missing platoon of marines highlighted itself on the ship's main viewport. Coordinates came next and a mission description. She set in the coordinates and took off.

The ship descended through the atmosphere, the air on Aether was much thicker than the thin aired Zebes or the normalcy of Earth. The planet had a blue-grey tinge to it, but that was always short-lived as Dark Aether came into and out of existence. The purple planet had a much more dramatic look to it; the entire outer atmosphere consisted of lightning storms that sent blue bolts tearing through the atmosphere and crashing into the surface. Every other second the makeup of the atmosphere would cycle through those two; rain, then lightning, never completely one or the other.

Then the atmosphere seemed to make up its mind and stayed with the composition and ferocity of Dark Aether, there was the crash of thunder and an explosion of light encircled the ship. Samus, even with the ship filtering the light, was blinded. When her vision returned the ship was back in the atmosphere of normal Aether, in mid freefall. She grabbed at the controls frantically, trying every trick in the book to slow or stop the ship before it crashed into the planet's surface. Nothing was responding, the control panel was sparking and shocking Samus's hands. With her hands bleeding, she activated her Power suit in hopes that it would protect her from the initial impact. Then the planet's surface contracted under her ship's weight and broke. Samus's helmet collided with the control panel, sending pain to the base of her neck. She staggered out of the command chair and towards the exit lift. Expecting hostile life-forms to be surrounding her ship, Samus exited with a flip, already scanning the area for potential threats. When she found none, she turned around and scanned her ship using her visor scanning device. It was heavily damaged and would be unable to fly for a very long time. She continued to explore the planet and found a dead squad of marines. Then, out of nowhere, a pseudo Samus, clad in a blue and glowing power suit, appeared before her, opening a portal before glancing back to her and entering. Samus followed and had her first look at her new nemesis, Dark Samus.

_Present_

"Well Samus, what do you think?" asked Jake

Samus shook off the memories, "They're giving me extreme nostalgia."

Jake laughed, "Well then you should remember that these types of machines prevented the pirates of Aether from gaining control of the sky temple."

Samus smiled, "Yeah, they did their job well, sure as hell gave me a rough time."

Derek cleared his throat, "Well, if you don't mind Samus, I still have to introduce the rest of the team."

Samus waved goodbye to Jake before following Derek out of the secret room and back into the lift platform.

"You guys have really out done yourself this time." Said Samus, "With this kind of tech fighting for the federation, you'll have the Pirate confederacy on the run in no time."

Derek nodded, "Yeah, once this is all on the front lines we'll make short work of the pirates. Having most of the Utrazonian branch wiped out during the Phazon crisis really gave us the edge, now we out number them and soon we'll out class them as well."

"And with Ridley gone, they no longer have control over the Zebesian branch too, that just leaves the Reptilians and the Insectoids."

The lift stopped and the pair walked into the next floor.

"But the Pirate High command is still intact." Explained Derek with a frown, "Which is why we've been experimenting with stealth tech."

"Stealth tech?" asked Samus "Is the Federation planning an assassination of the High command?"

While they were talking a marine started following them, neither Samus nor Derek seemed to take notice.

Suddenly Samus turned abruptly and pointed her newly materialized energy pistol at the marine, who backed up.

"I'd know that smell anywhere!" Said Samus, "Show your true form!"

The marine made a girlish chuckle before a cloud of purple vapor surrounded the marine, when the vapor had dissipated a woman was standing in the marine's place. Her internal organs where partially visible through her transparent purple skin. She had a standard blue federation insignia on her breast.

"I was wondering when you'd notice me." Said the girl with a grin

Derek placed his hand on Samus's energy pistol, "She's a friend Samus, lower the weapon."

Samus did what Derek asked, but kept it in hand instead of dematerializing it back into her zero suit.

"Who are you?" asked Samus

"My name is Fauna; I am the leader of the S.A.S." Explained Fauna, "If you don't know, that stands for Stealth and Assassination Squad."

"I know what it stands for." explained Samus, "You're one of Gandrayda's kind."

Fauna chuckled, "Yup, you got me."

Samus tightened her grip on the energy pistol, "This isn't funny Fauna, Gandrayda was the only one of the bounty hunters that willingly gave into her phazon possession and didn't make any attempt to help before completely giving in and attacking me."

Fauna put her hand on her hip and tilted her head, "I suppose that you're right about that, so it's only logical that you won't trust me."

Samus intensified her stare at Fauna, "If you want me to trust you, you'll have to earn it."

Derek put his hand on Samus's shoulder, "Let it go for now Samus, they're no reason for you to not trust-"

"She has every reason not to trust me!" Fauna suddenly said, "If she wants me to earn her trust, then I will; it sounds fun to me."

With that, Fauna started to walk back towards the elevator that Derek and Samus had come from. Derek started in the opposite direction, but Samus stayed still.

"Fauna," said Samus without moving to look at her, "If you do anything suspicious…"

Samus and Fauna turned to face each other.

"I'll kill you."

Fauna smirked and continued on her way while transforming into a marine again. The elevator doors closed and Derek let out a sigh.

"Man, you two give this place such a tense atmosphere."

"Sorry, please continue."

Derek looked at the ground while rubbing the back of his head, "What were we talking about?" asked Derek with a chuckle.

"Federation stealth tech." reminded Samus

They continued down the corridor, Derek leading with Samus closely in tow behind him. As they reached the end, a tall marine turned the other corner and bumped into Derek. Derek looked at the marine, who was a good foot taller than him and smiled before turning to Samus.

"This is our heavy weapons expert, Anthony Higgs." Explained Derek

The marine took off his helmet revealing his broad smile and dark skin. He had lightning bolts cut into the sides of his marine buzz-cut. He reached his hand out to Samus in a quick motion.

"Nice to meet you Princess!" Exclaimed Higgs as he shook her hand.

"Princess?" Samus repeated questioningly, "Is that some kind of joke?"

Higgs shook his head, never losing his smile, "Your hair," he said while motioning to her long blonde ponytail, "It makes you look like a Princess."

Samus blushed but other than that, her face remained the same. She then watched him as he continued on his path down the corridor, past her and Derek.

Derek touched her shoulder to get her attention back to him. She half jumped half shuddered when he touched her.

"Right, we should keep going." Said Samus

"Well, as I was saying before, the Federation has been working on strengthening its stealth department. While we do not have the power to take them head on yet, the pirates took a major blow thanks to the loss of their home-world during the phazon crisis." Explained Derek, "But as a result they've been tightening all of their remaining troops' defenses and holing up on rim planets. We had been monitoring pirate movement on Planet K2-L for years, but their defense has been impenetrable. Until recently: a small cargo ship has left the planet, our scans of the ship have shown that only 15 life-forms are on board."

Samus stopped dead in her tracks before looking directly at Derek, "There are 15 members on the Pirate second level of command."

Θ

The pirate command works in levels, they started with 3 levels, but the 3rd was annihilated a few years ago, the pirate second level of command is the one that oversees biological and other experiments and also is in charge of running the spy and reconnaissance missions. They usually keep a very low profile and have only been encountered once by Federation troops, unfortunately the entire flotilla of ships the Federation sent to kill or capture the second level was decimated by a high command member, Ridley. Ridley was a General of the pirate army and personally directed all of their attacks on the Federation and others. Samus has seen Ridley's body functions stop many times by her hand, but the Pirates have developed a way of resurrecting him. Even though she left no body or spec of DNA of him left after their battle on the pirate home-world, she doubts that he's really done for good.

Θ

"Do we know where the ship is now?" asked Samus, wide eyed with the thought of killing the second level.

"We know its trajectory, and in fact, we're tailing them with a cloak on right now." Explained Derek

"We're going to attack them, right?" Demanded Samus, "This ship is fully capable of taking on a cargo barge, right!"

Derek continued on his path without looking back, "Where to you think I've been leading you, the tour ends on the bridge."

Samus nodded and followed him through a huge double door that required Derek's retinal scan to open. The doors opened and the Bridge came into view, they were elevated over four stations, Samus knew the layout well, the two center stations were for communications and navigations, the two side ones were for weapons, one for the smaller hydra-class batteries and another for the large anti-shield and hull piercing weapons. Samus could only guess what those weapons would be on the _Ragnarok,_ an experimental all purpose vessel capable of handling pirate attack ships of the highest caliber. Captain Skylar stood a few feet in front of Samus and Derek, at the command post, overseeing all actions and scanning the vast void that was ahead of them.

"We're scanning the ship more directly to see if the life readings match the ones transmitted to us three years ago before Ridley…well anyway, if they match, we'll try to board the ship, if not we'll follow it to its destination, might lead us to a pirate base or something." Explained Derek

Samus and Derek stared at the huge view-screen in front of them for about a minute before a small brown dot came into view.

"That's it, isn't it?" Said Samus

"Yes," answered Skylar, "Don't worry, both our visual and radio is camouflaged thanks to our newest Stealth tech, designed by Fauna and Jake."

Samus's eyes went wide as she remembered the one fatal flaw in Gandrayda's camouflage…

Ω

Phazon Crisis

Before Federation's attack on the planet

_Samus had followed the marine for a few minutes now, he had apparently been a prisoner on the planet. He was leading Samus to the defense shield's generator, they ascended in an elevator into a room that was open aired, the acid rain lining the edges of the room. The marine aimed his gun at Samus, who rolls into a ball and unfurls with her cannon pointed at him. Maniacal laughter is heard from the marine, who transforms back into her true form, Gandrayda. _

"_You know, you should never trust strangers Sammy. This is going to be fun" said Gandrayda as the fight commenced. She transforms into Hunter Ghor and mimics his attacks, infuriating Samus even further. As Samus's constant shots damage her, Gandrayda becomes invisible. Samus changes to her heat and X-ray visor that she stole from the pirates. She is able to see Gandrayda clearly as she jumps onto Samus and electrocutes her._

Ω

Present

Samus runs up to Skylar, "They can see us!" she says hurriedly

Skylar turns back around and looks at Samus, "What are you talking about?"

"When I fought Gandrayda, I was able to see through her cloaking using a visor variant that I stole from the PIRATES!"

Skylar's eyes widen some, then go back to normal as he orders the crew to battle stations.

The crewman on the radio station piped up, "Sir they're raising shields and turning around to face us. They're charging weapons as well!"

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	3. Chapter 3

Chapter 3

Skylar leaned down from the command podium as if it would help get his orders across faster.

"Power up all weapons, get ready for battle!" yelled Skylar, "Deploy two Griffin classes to surround the enemy, we can't let the escape!"

The radio station trooper spoke up, "Sir, I'm getting some strange readings on the ship, some kind of radiation I think, but it's off the charts!"

"Never mind that now soldier, we'll do a scan of the ship after we disable her." Said Skylar

Flaps opened on the front of the pirate barge, all around the dark glass of their main viewport. More cannons, exact replicas in shape and size to the two originals, appeared. The cannons charged a central shot of energy, which easily outgrew the size of the pirate barge's viewport.

"Get the shields up, and then get me a reading on that energy sphere!" yelled Skylar from his podium

The energy sphere changed color from red to blue and fired, a slow moving attack, it looked ominous, growing closer and closer with every second.

"SIR!" yelled the radio man, "It's an EMP blast!"

Skylar, looked at the sphere with defeat, "You smart son of a bitch"

The EMP hit the _Ragnarok_ and all at once everything stopped, lights turned off, machines stopped whirring and whistling. The radio man started, "Our shields weren't at full power, and the blast has knocked out everything on the ship."

Skylar hung his head, "We're sitting ducks."

"Wait, wait SIR!" piped the radio man, "I've got several active readings coming from Jake's storage room, one of which is a ship!"

Derek turned to Samus, "The Anhur."

Samus nodded and they were off, running down the corridor at top speed, until they reached an inactive elevator. Samus pressed the Chozo insignia on her breast, and the Varia suit materialized in cinematic fashion. With the suit active, Samus pressed a button on her helmet, scanning and hacking the elevator into functioning again. They stepped onto the elevator and waited for its descent to end. When it did, they ran down the corridor and up to Jake's first door. Derek pressed the retinal scanner, but there was no response thanks to the EMP. Samus hacked the terminal with her scan visor and they started inside, but Jake once again had the blast doors up. Derek banged his suited fist on the door.

"Jake, open up, we need to borrow the Anhur!"

"No way in hell Derek!" came a muffled cry, "You'll get ripped to shreds out there!"

There was a pause, "Let me rephrase that, my SHIP'LL get ripped to shreds out there!"

Derek paused in defeat for a moment, and then smiled behind his visor, "Did you forget that you'll get to show Samus your ship?"

There was a cried of ecstasy and the blast doors opened. Jake stood before them, suit active.

"Let's go, I'll drive." Said Jake as he jogged to the Anhur

Samus and Derek stepped into the ship following Jake, who had gone to the flight terminal at the front of the ship. Derek quickly went to the back of the ship, and sat down into a weapons control terminal. Jake motioned for Samus to sit in the co-pilot's seat.

"Hold on tight, we'll have to make this a speed run." Explained Jake

They flew at top speed out of the docking bay, gaining altitude and then hovering over the top of the _Ragnarok_. Jake pushed the joystick into the terminal, shooting the Anhur straight at the Pirate Barge. The barge was charging up another shot from the communal cannons, this one was red. Samus scanned it quickly to see what it might do to the _Ragnarok._

_Target is a highly condensed sphere of plasma energy._

Samus wanted more information and the suit read her thoughts, elaborating on the weapon as it gains more information.

_Once contact is made with anything other than itself, the energy re-expands causing extreme damage to whatever it is fired at._

"_What effect will it have on the Ragnarok?"_ Samus thought

_The Ragnarok_ _will, in its current state, be destroyed completely._

"Jake!" said Samus, "I just did a scan on that attack, if it hits the Ragnarok…"

"I know." Said Jake calmly, "That's why…"

He drove the Anhur directly in front of the Pirate Ship's energy sphere.

"…I have to do this!" finished Jake

Jake punched a button and the Anhur's viewport flooded with blue. The pirate attack fired, and engulfed the Anhur completely, it then shrunk down. The Anhur remained intact and unaffected, besides being covered with a massive blue energy shield.

Samus put her arms down from in front of her head, a last defense that any human will try. She looked at Jake and saw him smiling from behind his visor.

"It worked, as expected…" said Jake with a chuckle, "MY INVENTION WORKS!"

"Just what the hell did you do?" asked Samus, "Why are we alive and intact?"

"It's an invention of mine, I call it 'Draining Shield'" explained Jake as he smoothly piloted the Anhur towards a docking bay, "It absorbs energy attacks and uses the power gained from that to super-charge the Anhur's shields and weapons."

They hovered for a minute, the docking bay doors locked in place before them. In the back of the ship, Samus heard Derek moving the weapons terminal.

"Ready to fire, Jake!" cried Derek from the back of the ship, "Firing!"

Blue lances of energy shot out of the Anhur's two parallel wings and from a few guns just under the viewport. The shots had almost no effect, other than some scorch marks. Jake rubbed his head.

"The Draining Shield should have super-charged the weapons as well as the shields…" thought Jake out loud, "Oh right, I was going to install that one next week."

"What!" yelled Derek from the back, "You mean that we can't get inside the pirate's ship?"

"I'm afraid not."

Just as all hope seemed lost, several blue energy blasts hit the docking bay doors and they fell into the abyss of space. A stiletto class fighter flew into the now open docking bay and landed.

"Who was that?" asked Derek

"Doesn't matter, get ready to board!" replied Jake

"Alright," said Samus as her arm cannon materialized, "Time for some fun."


End file.
